Anti-cooperative interactions in single-strand oligomers of deoxyriboadenylic acid

✍ Scribed by John N. Vournakis; Douglas Poland; Harold A. Scheraga

• Publisher: Wiley (John Wiley & Sons)
• Year: 1967
• Tongue: English
• Weight: 943 KB
• Volume: 5
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1967.360050502

✦ Synopsis

Optical rotatory dispersion measwements were made on the deoxyribo niicleot.ide$ d(pA)p, d(pA)r, d(pA)B and poly(deoxyriboadeny1ic acid) at, neutral pH over the temperature range 5-80°C. and were compared to similar data for the analogous oligoriboadenylic acids. The data were interpreted in terms of a temperature-dependent stacking of the bases in the single-strand deoxyribo oligomers. The thermal trarwitioii ciirves show an inverted chain-lengt,h dependence compared to the ribo oligomer cnrves. These results are explained by a theory of anti-cooperative int,eraction, where the nucleation parameter u is >l. The theory, based on a one-dimensional Iding model involving both attractive nearest-neighbor and repulsive next-nearest-neighbor interitctions, predicts the inverse chain length dependence and agrees rather well with the experimental data. At and above the transition temperature, the deoxyribo polymer i* seen to consist of isolzted stacked base pairs separat,ed by at least one unit of random coil, there being only a very small probability for the existence of sequences of stacked residues longer than one. The partition function is seen t.0 undergo ail irregalar behavior as a fnnction of chain length because of the anti-cooperative phenomenon. I t is necessary to use an enthalpy of stacking of -5.0 kcal./mole in order to fit the experiniental data wit.h t.he theory. This value, 1.5 kcal./mole more positive than the AH found for the ribo oligomers, is reasonshle, since the 2' hydroxyl group would he expected to stabilize the stacking interaction in the ribo oligomers. Various kinds of distribution fiinTtions are calculated and plotted graphically for t,his theoretical model. A physical rationale is presented for the use of a repulsive next-nearest-neighbor term in thL theory for the deoxyribo oligomers.